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Cryo-EM structure of Aquifex aeolicus RseP E18Q mutant in complex with Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold experimental model PDB 6AKQ experimental model PDB 3WKM experimental model PDB 8ZAY
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.9306 f_angle_d 0.6705 f_chiral_restr 0.0442 f_plane_restr 0.0045 f_bond_d 0.0028
Sample RseP ortholog E18 mutant in complex with 4A9 Fab Sample Components Fab of mouse monoclonal antibody IgG 4A9 RseP orhtholog E18 mutant from Aquifex aeolicus unknown peptide
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 120267 Reported Resolution (Å) 3.61 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (6AKQ, 3WKM, 8ZAY, 8ZAY) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 60
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 1800 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 0.024 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 105000 Calibrated Magnification 103703 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.4.0 IMAGE ACQUISITION SerialEM 4 CTF CORRECTION cryoSPARC 4.4.0 MODEL FITTING UCSF ChimeraX 1.71 MODEL FITTING Coot 0.9.8.92 MODEL REFINEMENT PHENIX 1.21_5207 INITIAL EULER ASSIGNMENT cryoSPARC 4.4.0 FINAL EULER ASSIGNMENT cryoSPARC 4.4.0 CLASSIFICATION cryoSPARC 4.4.0 RECONSTRUCTION cryoSPARC 4.4.0
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 4429254